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Table 1 Number of differentially expressed genes. Numbers of identified differentially expressed genes in the GP and GOT models after preprocessing by 0 or more MIDAS pipeline steps — IIV, IIVT, IIVTL, IIVTLS, or IIVTSLF. For Experiment 1, up-expression (+) and down-expression (-) numbers are given for both WT and antiPLD. For Experiment 2, + and -1 numbers are given for all 4 genotypes separately. The ALL entries correspond to the H1 hypotheses of the GOT model (see Materials and Methods).

From: The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

Genotype   IIV IIVT IIVTL IIVTLS IIVTLSF
   GP Model — Experiment 1
WT + 567 571 487 495 460
WT - 552 553 499 499 460
antiPLD + 442 421 440 471 431
antiPLD - 336 346 381 363 334
   GOT Model — Experiment 2
Col-0 + 227 309 242 240 270
Col-0 - 122 171 178 180 183
Cvi-0 + 106 108 82 78 71
Cvi-0 - 63 93 74 71 67
WS + 234 346 279 269 150
WS - 331 347 340 340 224
Th + 238 398 350 363 361
Th - 196 245 241 246 240
ALL + 298 428 357 354 290
ALL - 202 261 253 248 195